reticulation coding, etc.

[Ken Kinman]

     I only coded higher level reticulation in my book, since it only
classifies organisms from Kingdom down to Order level.
     But my bacterial classification clearly shows the origins of eukaryotic
organelles:
     mitochondria from Proteobacteracea
     peroxisomes from Posibacteracea
     primary chloroplasts from Cyanobacteria
     cytosol (host cell) from Metabacteria ("Archaea")
     ??cilia from Spirochaetea (doubt expressed on this,
          but Lynn Margulis still holds that view).
---BTW, the preponderance of the evidence indicates that the eukaryotic host
cell evolved from Class Crenarchaea (Phylum Metabacteria), which are
synonymous with Jim Lake's "eocytes".  Lake's ideas still have some problems
(IMO), but he has always been closer to the truth than Carl Woese.  It takes
a lot of perseverance to overcome various "Woesian" misconceptions, but some
of us in microbiology are certainly trying.
     Anyway, if I can classify the origins of such complex reticulations as
those, similar conventions can be adapted to hybridization at species level.
     And as for polytomies, I found that coding them with the repetition of
a letter works well (as in the trichotomy of X1, X2, and X3 below):
   1  Taxon X1
   A  Taxon X2
   A  Taxon X3
   2  Taxon Y
   3  Taxon Z
******************************************************
     I am enough of a cladist to believe that such polytomies do not exist
at higher taxonomic levels.  Even among rapidly radiating taxa (e.g.,
post-Cretaceous mammal orders and families), a dichotomous branching will
eventually emerge given enough fossil data.  But until you do have enough
data, you must sometimes either label such polytomies as "sedis mutabilis"
(E.O. Wiley) or use the equivalent Kinman coding (repeated letters).  Take
your pick.  When more information is available, the coding can be changed to
reflect the full nested series (but without having to create new categories
and names).
     Although I do find cladistic analysis extremely valuable, I have always
hesitated to call myself a cladist, because I never had that distaste for
paraphyletic groups drilled into me.  The use of Kinman markers to render
them semi-paraphyletic (with sister group information explicitly included)
is at very heart of the Kinman System, and therefore I now find most of the
bickering between cladists and eclecticists to be not only unproductive, but
much of it is now totally unnecessary.
                   ------Ken Kinman
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